title: ChIP-seq of TCF7L2 in human GPC

city: Rochester

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description: ChIP-seq

data_processing:
The sequencing reads were pre-processed by trimming off adapter and low-quality bases using fastp (Chen et al., 2018). Reads were then aligned to the human genome assembly GRCh38 or the rat genome assembly Rnor6.0 using bowtie2 (Flicek et al., 2014; Langmead and Salzberg, 2012). Following alignment, reads with low alignment quality were filtered using samtools (Li et al., 2009). Aligned reads were then assessed for enrichment in specific genomic regions, where peaks were called with MACS2 (Zhang et al., 2008).
Genome_build: GRCh38
Supplementary_files_format_and_content: bw
Supplementary_files_format_and_content: .narrowPeak

source_name: GPC induced from ESC

growth_protocol: GPCs were generated from human embryonic stem cells (ESCs) using our previously described protocol (Wang et al., 2013, Windrem et al., 2017).

extract_protocol: Chromatin immunoprecipitation was carried out following Pedersen et al, 2016 with minor modifications. Briefly, freshly sorted GPCs were cross-linked using 37°C pre-heated medium/1% formaldehyde. Fixation was carried out at room temperature for 10 minutes, and reaction was terminated with 0.125 M glycine, followed by two PBS washes. The cross‐linked cells were lysed in SDS lysis buffer containing protease inhibitors (PMSF, Aprotinin and Leupeptin). Nuclei were then pelleted and resuspended in ice-cold IP Buffer (2:1 SDS:Triton dilution buffer). DNA were sonicated using a Diagenode biorupter pico (30 min ON, 30 min OFF for 5 cycles) to an average length of 200–700 nucleotides. DNA was subsequently incubated overnight with the appropriate antibodies (OLIG2 or TCF7L2), and immunoprecipitated the next day with Protein-G. Three washes in low‐salt wash buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 2 mM EDTA, 20 mM Tris–HCl pH 8), and three washes in high‐salt wash buffer (500 mM NaCl, 1% Triton X‐100, 0.1% SDS, 2 mM EDTA, 20 mM Tris–HCl pH 8) were carried out, followed by de-crosslinking at 65°C for 8-16 hours with SDS buffer (1% SDS, 0.1 M NaHCO3). DNA was purified using the Qiagen PCR Purification kit.  Libraries were prepared with the NEBNext Ultra II DNA library preparation kit (NEB#7645) following manufacturer’s protocols.

tag: antibody


title: Horse 15, non-immune, d18pi

status: Public on May 08 2024

type: SRA

city: Ithaca

first: Bettina

last: Wagner

state: NY

address: 240 Farrier Drive

department: Population Medicine and Diagnostic Sciences

country: USA

institute: Cornell University

description:
NE54-Horse15-D18pi
equine_rawCounts.txt

library_source: transcriptomic

data_processing:
Initial processing was carried out Cornell University’s Transcriptional Regulation and Expression (TREx) facility
Reads were trimmed for loq quality and adaptor sequences using TrimGalor v0.6.0, cutadapt, and fastQC.
Equine sequences were aligned using STAR v2.7.0e, to generate a raw counts table.
SARTools and DESeq2 v1.26.0 was used to generate normalized counts and statistical analysis of differential gene expression. Raw counts were additionally analyzed in iDEP.951, to determine differential expression
Viral sequences were aligned to the EHV-1 Ab4 genome (NC_001491.2) and a raw counts table was generated usinghtseq-count (Galaxy Version 0.9.1)
Assembly: EquCab 2.0
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

molecule: total RNA

organism: Equus caballus

source_name: nasal mucosa

extract_protocol:
RNA was extracted using TRIzol LS reagent (Life Technologies Corporation, Carlsbad, CA, USA) following the manufacturer’s protocol.
RNA was processed using NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) to create a cDNA library, which was quantified with a Qubit 2.0 (dsDNA HS Kit, Thermo Fisher, Waltham, MA, USA) and fragment size distribution was determined by Fragment Analyzer (Advanced Analytical, Orangeburg, NY, USA).

treatment_protocol: All horses were intranasally infected with 1x10^7 PFU neuropathogenic EHV-1 Ab4 on d0.

tag: tissue

value: nasal mucosa

tag: treatment

value: EHV-1 Ab4 challenge

tag: time

tag: immune status

value: non-immune

tag: breed

value: Icelandic


title: WT non-treated control 1

city: San Diego

first: Paulo

middle: VG

last: Alabarse

state: CA

address: 9500 Gilman Drive

department: Rheumatology

institute: University of California, San Diego

data_processing:
Cutadapt and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HISAT2 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-96/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie
Assembly: All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Supplementary files format and content: Excel file include FPKM values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Bone marrow derived macrophages

growth_protocol: Isolated mouse bone marrows were cultured in RPMI containing 10% FBS, penicillin (100 U/ml), streptomycin (100 μg/ml) and 20% L929 conditioned media for 7 days. After priming with GM-CSF (20 ng/ml) for 24 hours, cells were washed with PBS and subjected to experiments in RPMI containing 1% FBS.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA samples were sent to LC sciences for RNA-seq
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library was then constructed.

treatment_protocol: WT BMDMs in the presence or absence of apigenin (25 uM) and CD38KO BMDMs were stimulated with MSU crystals (0.2 mg/ml) for 6 hours.

tag: cell type

value: Bone marrow derived macrophages

tag: genotype

value: WT


title: A375_DMSO-DMSO-0_R3

city: Lyon

first: Nicolas

last: Fontrodona

address: 46 allée d'Italie

country: France

institute: ENS de Lyon

data_processing:
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 20 -3 --cut_tail_window_size 10 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA –adapter_sequence=AAAAAA)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10  -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

molecule: cytoplasmic RNA

organism: Homo sapiens

growth_protocol: A375 cells were obtained from ATCC and cultured in DMEM containing all amino-acids except glutamine (Gibco, 10938025) and supplemented with 10% FBS, 2mM glutamine and penicillin-streptomycin, at 37°C and 5% CO2. Cells were passed at around 80% confluency, 3 times a week.

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
We prepared QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, LEX113.96) libraries from RNA samples following the manufacturer’s instructions. 500ng of RNA were spiked-in with 1µL of a 1:100 dilution of ERCC Spike-In Mix (ThermoFisher, 4456740) before the library preparation. Libraries were then quantified, pooled and sent for sequencing at Novogene (Novaseq 6000 1x150)

treatment_protocol: Cells were plated and the following day, the culture medium was removed and replaced with fresh medium containing 1µM vemurafenib and cobimetinib (500nM vemurafenib + 500nM cobimetinib) or DMSO. 18h later, cells were treated with fresh cycloheximid (100µg/ml) or DMSO. 5 minutes later, cells were treated with tryptolide (25µM) or DMSO, making a total of 2x2x2 = 8 samples so far. This was prepared in 4 identical batches A B C D, and batch A was immediately harvested after +/- tryptolide treatment (T0 samples). Batches B, C and D were harvested 1h, 3h and 5h later, respectively (samples T1, T3 and T5).

tag: cell line

value: skin melanoma

value: DMSO followed by DMSO treatment for 0 hours


title: ChIP-seq of OLIG2 in human GPC

first: Steven

description: ChIP-seq

library_source: genomic

molecule: genomic DNA


title: WT non-treated control 2


title: WT MSU treated control 3

value: MSU


title: A375_DMSO-DMSO-1_R1

value: DMSO followed by DMSO treatment for 1 hours


title: Horse 6, immune, d18pi

description:
NE51-Horse6-D18pi
equine_rawCounts.txt

value: immune


title: A375_DMSO-DMSO-0_R2


title: WT MSU treated control 2


title: Horse 24, immune, d10pi

description:
NE48-Horse24-D10pi
equine_rawCounts.txt


title: geo_submission_miRNA-seq april 27

city: Guangzhou

first: Yingying

last: Xiao

state: Guangdong

address: A2-652, Guangzhou Medical University, Xinzao Road, Panyu District, Guangzhou

department: the School of Pharmaceutical Sciences

country: China

institute: Guangzhou Medical University

data_processing: De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).  The differentially expressed miRNAs (DEG) between FA to O3, males and females were identified by using the edgeR (Robinson et al., 2010) and the TCC v1.14.0 R package (Sun et al., 2013) with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.

source_name: mouse embryo

extract_protocol:
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3.
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

value: mouse embryo

value: cells cultured in vitro

value: cardiopulmonary progenitors

value: culture in vitro without other treatment


title: WT MSU treated control 1


title: A375_DMSO-DMSO-0_R1


title: Horse 20, non-immune, d10pi

description:
NE47-Horse20-D10pi
equine_rawCounts.txt


title: Horse 15, non-immune, d10pi

description:
NE46-Horse15-D10pi
equine_rawCounts.txt


title: UUO #2 10 days

city: San Juan de Alicante

first: Angela

last: Nieto

state: Alicante

address: Av. Ramón y Cajal s/n

department: Developmental Neurobiology

country: Spain

institute: Instituto de Neurociencias (CSIC-UMH)

description: single-cell gene expression profiling (scRNA-seq)

data_processing:
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software [[2.2.58]]. HiSeq Sequencing v4 Chemistry. Read Length: 75 paired end
Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger (v.2.2.0) pipeline (10x Genomics) and aligned to the CRGm38 (mm10) mouse reference genome customized to also count reads in WPRE exogenous sequence as a cancer cell tdTomato reporter (gene annotation version 99. We retrieved 310M reads per sample, 61% reads mapped confidently to exonic regions, 9K mean cells per sample, 34K mean reads per cell, 2.7K mean median unique counts per cell and sample, and 1.1K mean median genes per cell and sample.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: Single-cell RNA-seq datasets. Each dataset contain three files: barcodes.tsv (a tab separated values file with cellular barcodes present in dataset); genes.tsv (a tab separated values file with IDs of quantified genes (Mouse ENSEMBL Gene ID and Gene Symbol); matrix.mtx (a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes). A standard or sparse matrix can be generated where genes.tsv file correspond to the genes or row names of the matrix, while barcodes.tsv corresponds to the cell or columns.

source_name: Whole kidney 10 days post UUO

extract_protocol:
Kidneys were collected and subjected to single cell disregation protocol as described in Youssef et al. 2021.
Single cell preprartion from whole kidney were processed to generate cDNA libraries according to Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol (10X Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads.
scRNA-seq (single-cell RNA-seq)

treatment_protocol: 12 weeks mice males were subjected to UUO or SHAM. After 10 days, obstructed kidneys or SHAM control were harvested and single-cell RNA-seq was performed on the whole kidney.

tag: strain

tag: age

value: adult 12 weeks

tag: Sex

value: Male


title: UUO #1 10 days


title: SHAM 10 days

source_name: Whole kidney 10 days post SHAM


title: WT Apigenin and MSU treated 3

value: Apigenin


title: A375_DMSO-CHX-5_R3

value: DMSO followed by cycloheximid treatment for 5 hours


title: Horse 11, immune, d10pi

description:
NE44-Horse11-D10pi
equine_rawCounts.txt

value: nasal mucosa

value: EHV-1 Ab4 challenge


title: A375_DMSO-CHX-5_R1


title: Horse 6, immune, d10pi

description:
NE43-Horse6-D10pi
equine_rawCounts.txt

value: Icelandic


title: A375_DMSO-CHX-3_R2

value: DMSO followed by cycloheximid treatment for 3 hours


title: WT Apigenin treated 3

value: Bone marrow derived macrophages

value: WT

value: Apigenin+MSU


title: WT Apigenin and MSU treated 2


title: WT Apigenin treated 2


title: WT Apigenin and MSU treated 1


title: Horse 5, non-immune, d10pi

description:
NE42-Horse5-D10pi
equine_rawCounts.txt

value: non-immune


title: Horse 14, immune, d10pi

description:
NE45-Horse14-D10pi
equine_rawCounts.txt

value: immune


title: T2 Mammary_gland_tumour

data_processing:
Sequencer: Illumina HiSeq 2500. HiSeq Sequencing v4 Chemistry. Read Length: 75 paired end.
Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger (v.2.2.0) pipeline (10x Genomics) and aligned to the CRGm38 (mm10) mouse reference genome customized to include reporter transgene (tdTomato including WPRE sequence). Genome annotation version 99. We generated 4 libraries. Each library was performed from a mammary carcinoma isolated from three independent mice. We profiled a total of 36,162 cells (T1:8,724 cells; T2:9580 cells; T3:8434 cells; T4:9424 cells). Libraries were sequenced to obtain more than 1.200 million reads in total (T1:>313M; T2:>313M; T3:>306M; T4:>308M). In all four libraries, mean read pairs per cell was above 30,000 (T1:35,878; T2:32,730; T3:36,377; T4:32,731). Confident mapping to exonic regions was higher than 61% for each library. For each library, median unique counts per cell was as follows: T1:1,922; T2:3,281; T3:2,854; T4:2,589; and median detected genes per cell was as follows: T1:842; T2:1,321; T3:1,142; T4:1,079.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: Single-cell RNA-seq datasets. Each dataset contain three files: barcodes.tsv (a tab separated values file with cellular barcodes present in dataset); genes.tsv (a tab separated values file with IDs of quantified genes (Mouse ENSEMBL Gene ID and Gene Symbol); matrix.mtx (a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes). A standard or sparse matrix can be generated where genes.tsv file correspond to the genes or row names of the matrix, while barcodes.tsv corresponds to the cell or columns.

growth_protocol: Mouse experiments were carried out on MMTV-PyMT (Guy et al., 1992; Lin et al., 2003), Rosa-tdTomato (Madisen et al., 2010) and K14Cre (Dassule et al., 2000), and back crossed in FVB background for 10 generations (99.9% FVB). Mice were fed ad libitum, handled and housed under the standard of the European Community Council Directive (2010/63/EU) and Spanish legislation.  Mammary gland-specific expression of PyMT under the control of the MMTV promoter/enhancer in transgenic mice (MMTV-PyMT) results in widespread transformation of the mammary epithelium and in the development of multifocal mammary adenocarcinomas and metastatic lesions in the lymph nodes and in the lungs (Guy et al., 1992). Tumor formation and progression in these mice is characterized by four stages: hyperplasia, adenoma/mammary intra-epithelial neoplasia, and early and late carcinoma (Lin et al., 2003). K14-Cre transgene that has a human keratin 14 promoter directing expression of Cre recombinase, trigger deletion of flexed sequences in the endoderm and its derivatives (Dassule et al., 2000). Rosa-tdTomato is a universal Cre-responder transgene with strong, ubiquitous expression of tdTomato fluorescent protein (Madisen et al., 2010).

extract_protocol:
Tumours where collected from Young adult (13-14-week-old) female MMTV-PyMT::K14Cre::Rosa-tdTomato mice, minced manually using sterile scalpels and further finely cut until homogeneous aspect using McIlwain Tissue Chopper (TED PELLA, INC). Minced samples where digested in digestion buffer (2,5ml for 1mg tumour) at 37ºC for 45 minutes on rocking plates chamber (reference VWR). Digestion buffer was based on PBS supplemented 2.5 Wünsch unit’s TH Liberase /ml (Roche) (50mg TH Liberase in 52 PBS = 5W unit/ml) and with 25μg/ml DNase I (Roche). To achieve single cells disruption, tumours fragments were pipetted up and down every 5 minutes. The progression of the cellular disaggregation was evaluate using microscope. Disaggregated samples were neutralized with 15ml breast medium supplemented by 25μg/ml DNase I and passed through a 70μm filter (BD Falcon) then 40μm filter (BD Falcon). Further, cells were spun down (5 minutes at 400 RCF at RT) and the pellet resuspended in 5ml of red blood lysis ACK (Ammonium-Chloride-Potassium) buffer for 5 minutes at RT with continuous gentINle rotation. After, cells were spun down and resuspended in 5ml FACS buffer/5mM EDTA and filtered through 40μm filter. 20μl of the cell preparation where mixed with equal volume of Trypan Blue and incubated for 5min to evaluate cells number and confirm the quality of single cells preparation, cell viability and low debris contains. Cells were further spun down (3 minutes at 400 RCF at RT) and resuspended in Dead cell removal beads (MiltenyiBiotec) at 100μl/10M and Incubated 15min at RT with gentle mixing. During the incubation, MACS LS column (MiltenyiBiotec) were placed on the magnet rack and conditioned by rinsing 1X with binding buffer 1X. After, cells were spun down (3 minutes at 400 RCF at 4C), resuspended in 3ml 1X binding buffer and applied on the magnetic column. Passing living cells (column retain the dead cells) were collected in 50ml Falcon tube placed in ice. Column where rinsed 4X with 3ml binding buffer to further living cells in the same Falcon tube. Collected cell were finally spun down (5 minutes at 400 RCF at 4C) and resuspended in cold breast medium and kept on ice. 20μl cells where mixed with 20ul trypan Bleu, incubate for 5minutes to count the proportion of viable and double check single cells state. Viability was first time evaluated on a BD FACS Aria III % as well as cancer cells, non-cancer cells and debris contains, and later, by measuring DAPI negative cells fraction. Finally, cells concentration was adjusted to 900-1000 cell/μl with cold FACS buffer and directly used for GEM (Gel Bead-In-Emulsions) preparation.
Individual cell encapsulation for single cell expression profiling was done using 10x Chromium Controller (10xGenomics). For every sample, single cell suspension was loaded into a Chromium Single Cell A Chip (10x Genomics) and processed following the manufacturer’s instructions. Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead kit v2 and samples were multiplexed using Chromium i7 Multiplex kit (10x Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads.

value: FVB

value: Female

value: Mammary gland

tag: condition

value: Tumour

value: mouse 2


title: T4 Mammary_gland_tumour

value: MMTV-PyMT (Guy et al., 1992; Lin et al., 2003), Rosa-tdTomato (Madisen et al., 2010) and K14Cre (Dassule et al., 2000)

value: mouse 3


title: A375_DMSO-CHX-3_R3

value: skin melanoma


title: T3 Mammary_gland_tumour


title: A375_DMSO-CHX-3_R1


title: A375_DMSO-CHX-5_R2

value: DMSO followed by cycloheximid treatment for 5 hours


title: Horse 3, non-immune, d10pi

description:
NE41-Horse3-D10pi
equine_rawCounts.txt

value: nasal mucosa

value: EHV-1 Ab4 challenge


title: A375_DMSO-CHX-1_R3

value: DMSO followed by cycloheximid treatment for 1 hours


title: T1 Mammary_gland_tumour

value: mouse 1


title: CD38KO non-treated 3

value: Bone marrow derived macrophages


title: TCR_Batch1, TCR V(D)J-enriched cDNA

city: Seattle

first: Chetan

last: Seshadri

state: WA

address: 850 Republican St

institute: University of Washington

library_source: transcriptomic single cell

data_processing:
GEX: Cell Ranger (v3.1.0, 10x Genomics) was used to conduct the alignment and feature expression quantification of the single-cell sequencing data. mRNA reads were aligned to the GRCh38-1.2.0 human reference genome. ADT reads were aligned to a feature reference containing the appropriate barcode sequences.
TCR: Cell Ranger (v2.1.1, 10x Genomics) was used to conduct the alignment and feature expression quantification of the single-cell sequencing data. V(D)J  reads were aligned to the GRCh38-alts-ensembl human reference genome.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger software output files: H5

source_name: PBMC

extract_protocol:
Single-cell library preparation for surface protein, mRNA,  and TCRs was performed using the Chromium Single Cell  V(D)J Reagent Kit v1.1 (10x Genomics). The TCR V(D)J  region was specifically enriched in a separate library preparation  using the Chromium Single-Cell V(D)J Enrichment Kit  (10x Genomics). Cell suspensions were combined with barcoded,  single-cell 5′ gel beads and loaded onto Chromium Next GEM  Chip G (10x Genomics) at a limiting dilution such that a single  bead and a single cell are partitioned into a sphere. Libraries were  sequenced by Illumina sequencing (NextSeq 500/550 platform).
GEX: Single Cell 5' R2-only. TCR: Single Cell V(D)J R2-only.

value: PBMC

value: unstimulated


title: A375_DMSO-CHX-1_R2


title: Horse 24, immune, d8pi

description:
NE40P-Horse24-D8pi
equine_rawCounts.txt

value: immune

value: Icelandic


title: Horse 20, non-immune, d8pi

description:
NE39-Horse20-D8pi
equine_rawCounts.txt

value: non-immune


title: CD38KO non-treated 2


title: A375_DMSO-CHX-1_R1


title: GEX4_Batch1, mRNA- and ADT-derived cDNA


title: CD38KO non-treated 1


title: GEX3_Batch2, mRNA- and ADT-derived cDNA


title: A375_DMSO-CHX-0_R2

value: DMSO followed by cycloheximid treatment for 0 hours


title: CD38KO MSU treated 3

value: MSU


title: Horse 11, immune, d8pi

description:
NE36-Horse11-D8pi
equine_rawCounts.txt


title: GEX3_Batch1, mRNA- and ADT-derived cDNA


title: Horse 14, immune, d8pi

description:
NE37-Horse14-D8pi
equine_rawCounts.txt


title: CD38KO MSU treated 2


title: A375_DMSO-CHX-0_R1


title: Horse 6, immune, d8pi

description:
NE35-Horse6-D8pi
equine_rawCounts.txt


title: CD38KO MSU treated 1


title: WT Apigenin treated 1

value: WT

value: Apigenin+MSU


title: GEX2_Batch2, mRNA- and ADT-derived cDNA


title: Horse 24, immune, d5pi

description:
NE32-Horse24-D5pi
ehv-1_rawCounts.txt


title: A375_BRAF-TCHX-5_R3

value: MAPK inhibitors followed by cycloheximid and tryptolide treatment for 5 hours


title: GEX2_Batch1, mRNA- and ADT-derived cDNA


title: AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse15_liver

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description:
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse15_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8

data_processing:
We mapped reads to mouse referenge genome mm10 provided by NCBI with bksnake, a Roche-internal analysis pipeline.
Differential gene expresison analysis was performed with edgeR.
Assembly: mm10
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-counts.gct: gene count table, in GCT format
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-sampleAnnotation.tsv: sample annotation, in TSV format
Supplementary files format and content: 20220925-RocheTUM-HBVTcells-featureAnnotation.tsv: feature annotation, in TSV format

source_name: liver

extract_protocol:
100 cells were directly sorted into 96 well plates prepared with 1X Reaction Buffer consisting of lysis buffer and RNase Inhibitor for low input RNA sequencing (Takara Bio USA). Plates were spun down and immediately stored on dry ice or at -80°C until further processing.
Sample plates containing lysed cells were subjected to cDNA library preparation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, USA) followed by sequencing library preparation using the Nextera XT DNA Library Preparation Kit (Illumina) as per manufacturer’s instructions with minor modifications. Briefly, full-length cDNA was generated by reverse-transcription, template-switching reaction and PCR pre-amplification of polyadenylated mRNA as previously described (Picelli et al. 2013). cDNA libraries were quantified using the Qubit dsDNA High Sensitivity Kit and quality was assessed on a Bioanalyzer using DNA High Sensitivity chips (Agilent Technologies). Double-stranded cDNA was subjected to fragmentation and PCR-based addition of Illumina barcoded sequencing adapters at both fragment ends. Sequencing library quantity and quality was assessed as described above.

value: liver

tag: simpletreatment

value: persistent AdHBV infection


title: A375_BRAF-TCHX-5_R2

value: skin melanoma


title: Horse 20, non-immune, d5pi

description:
NE31-Horse20-D5pi
ehv-1_rawCounts.txt

value: nasal mucosa

value: EHV-1 Ab4 challenge


title: AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse14_liver

description:
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse14_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8


title: GEX1_Batch2, mRNA- and ADT-derived cDNA


title: GEX4_Batch2, mRNA- and ADT-derived cDNA


title: Horse 15, non-immune, d5pi

description:
NE30-Horse15-D5pi
ehv-1_rawCounts.txt


title: AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse13_liver

description:
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse13_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8


title: A375_DMSO-CHX-0_R3


title: A375_BRAF-TCHX-3_R3

value: MAPK inhibitors followed by cycloheximid and tryptolide treatment for 3 hours


title: AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse12_liver

description:
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse12_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8


title: Horse 14, immune, d5pi

description:
NE29-Horse14-D5pi
ehv-1_rawCounts.txt


title: GEX1_Batch1, mRNA- and ADT-derived cDNA


title: A375_BRAF-TCHX-5_R1


title: A375_BRAF-TCHX-3_R2


title: A375_BRAF-TCHX-3_R1


title: 9D_S10

city: Pittsburgh

first: Colleen

middle: A.

last: McClung

address: 450 Technology Drive

institute: University of Pittsburgh

data_processing:
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of the data. Per base sequence quality was high (Quality score generally >30) indicating good data quality. HISAT2 (HISAT2v2.1.0) was used to align reads to the reference (Mus musculus Ensembl GRCm38) using default parameters. The resulting bam files were converted to expression count data using HTSeq (HTSeq v0.10.0) with default union mode.
Assembly: GRCh38
Supplementary files format and content: mouse_D1D2_logCPMfiltered_counts.csv
Library strategy: Ribo-seq

source_name: D1-expressing neuron

extract_protocol:
Brains from male and female mice were extracted and flash frozen across 6 times of day (ZT2,6,10,14,18,22). Bilateral 1-mm punches were taken centered over the NAc. Co-immunoprecipitation, as described previously (37,38), was used to isolate the ribosome-associated mRNAs from D1- and D2-expressing neurons. NAc tissue was pooled from 2 Drd1- and A2a-Cre (D2) mice per sample. Tissue punches were dounce homogenized withbuffer containing 50 mmTris, pH 7.4, 100 mmKCl, 12 mmMgCl2, and 1% NP-40 supplemented with 1 mmDTT, 100 μg/ml cyclohexamide, 1 mg/ml heparin, RNasinâ Plus ribonuclease inhibitor (200 units/mL; Promega), and EDTA-free protein inhibitor cocktail (Roche). Samples were centrifuged at 10,000gfor 10 min and the clear supernatant was transferred to low-protein binding tubes. Anti-HA antibody (40mg; Biolegend) was added to each lysate sample. Tubes rotated overnight at 4°C. On day 2, Dynabeads (400 mL; Invitrogen) were washed in homogenization buffer (un-supplemented) and added to the antibody-bound lysate samples. Tubes were again incubated overnight at 4°C with rotation. On day 3, magnetic beads were washed 3 times in a magnetic rack for 5 min in high-salt buffer (50 mmTris, pH 7.4, 300 mmKCl, 12 mmMgCl2, 1% NP-40, 1 mmDTT, and 100 μg/ml cyclohexamide). Finally, RNA was extracted from the bead-bound polyribosomes by adding TRK lysis buffer provided in the MicroElute Total RNA Kit (Omega) according to the manufacturer's instructions. Eluted NAc cell-type specific RNA was used for RNA-sequencing. Astrocyte-specific mRNA was previously collected as above (38), except that 20 mg of anti-GFP antibody (Abcam) was used. Homogenate RNA was previously collected. Samples were collected across time of day and punched as above, but without pooling. Tissue was homogenized and total RNA was isolated using the RNeasy Plus Micro kit (QIAGEN). RNA quantity and quality for all samples were assessed using fluorometry (Qubit RNA High Sensitivity Assay kit; Invitrogen) and chromatography (2100 Bioanalyzer and RNA 6000 Pico kit; Agilent).
Libraries were prepared with 10ng of RNA from each sample using the Smartseq HT ultra low input (D1 and D2) or Smartseq stranded total RNA ultra low input (homogenate) sample preparation kits (Illumina).

value: D1-expressing neuron

value: female


title: 9B_S3


title: Horse 5, non-immune, d5pi

description:
NE26-Horse5-D5pi
ehv-1_rawCounts.txt


title: 9A_S9


title: A375_BRAF-TCHX-1_R3

value: MAPK inhibitors followed by cycloheximid and tryptolide treatment for 1 hours


title: Horse 3, non-immune d5pi

description:
NE25-Horse3-D5pi
ehv-1_rawCounts.txt


title: AdHBV_resolved_CXCR6pos_CD45_1pos_CD8_mouse9_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse9_liver
AdHBV_resolved__liver__CXCR6pos_CD45_1pos_CD8

value: resolved AdHBV infection


title: A375_BRAF-TCHX-1_R2


title: 8D_S9


title: AdHBV_resolved_CXCR6pos_CD45_1pos_CD8_mouse7_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse7_liver
AdHBV_resolved__liver__CXCR6pos_CD45_1pos_CD8


title: 9C_S11


title: AdHBV_persistent_CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse11_liver

description:
CXCR6pos_CX3CR1pos_CD45_1pos_CD8_mouse11_liver
AdHBV_persistent__liver__CXCR6pos_CX3CR1pos_CD45_1pos_CD8


title: Horse 24, immune, d3pi

description:
NE24-Horse24-D3pi
equine_rawCounts.txt
ehv-1_rawCounts.txt

value: immune

value: Icelandic


title: A375_BRAF-TCHX-1_R1


title: 8C_S10


title: Horse 20, non-immune, d3pi

description:
NE23-Horse20-D3pi
ehv-1_rawCounts.txt

value: non-immune


title: AdHBV_resolved_CXCR6pos_CD45_1pos_CD8_mouse6_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse6_liver
AdHBV_resolved__liver__CXCR6pos_CD45_1pos_CD8


title: A375_BRAF-TCHX-0_R3

value: MAPK inhibitors followed by cycloheximid and tryptolide treatment for 0 hours


title: 8B_S2


title: Horse 6, immune, d5pi

description:
NE27-Horse6-D5pi
ehv-1_rawCounts.txt


title: Horse 11, immune, d5pi

description:
NE28-Horse11-D5pi
ehv-1_rawCounts.txt


title: Horse 15, non-immune, d3pi

description:
NE22-Horse15-D3pi
ehv-1_rawCounts.txt


title: AdHBV_persistent_CXCR6pos_CD45_1pos_CD8_mouse14_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse14_liver
AdHBV_persistent__liver__CXCR6pos_CD45_1pos_CD8


title: 8A_S8


title: A375_BRAF-TCHX-0_R2


title: AdHBV_persistent_CXCR6pos_CD45_1pos_CD8_mouse15_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse15_liver
AdHBV_persistent__liver__CXCR6pos_CD45_1pos_CD8


title: A375_BRAF-TCHX-0_R1


title: 7D_S8


title: AdHBV_resolved_CXCR6pos_CD45_1pos_CD8_mouse8_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse8_liver
AdHBV_resolved__liver__CXCR6pos_CD45_1pos_CD8


title: AdHBV_persistent_CXCR6pos_CD45_1pos_CD8_mouse13_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse13_liver
AdHBV_persistent__liver__CXCR6pos_CD45_1pos_CD8


title: Horse 11, immune, d3pi

description:
NE20-Horse11-D3pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: A375_BRAF-T-5_R3

value: MAPK inhibitors followed by tryptolide treatment for 5 hours


title: 7C_S9


title: AdHBV_persistent_CXCR6pos_CD45_1pos_CD8_mouse12_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse12_liver
AdHBV_persistent__liver__CXCR6pos_CD45_1pos_CD8


title: Horse 6, immune, d3pi

description:
NE19-Horse6-D3pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: A375_BRAF-T-5_R2


title: Horse 5, non-immune, d3pi

description:
NE18-Horse5-D3pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: A375_BRAF-T-5_R1


title: AdHBV_resolved_CXCR6pos_CD45_1pos_CD8_mouse10_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse10_liver
AdHBV_resolved__liver__CXCR6pos_CD45_1pos_CD8


title: A375_BRAF-T-3_R3

value: MAPK inhibitors followed by tryptolide treatment for 3 hours


title: Horse 3, non-immune d3pi

description:
NE17-Horse3-D3pi
ehv-1_rawCounts.txt


title: 6D_S7

value: male


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse9_spleen

description:
CX3CR1pos_CD45_1pos_CD8_mouse9_spleen
AdHBV_resolved__spleen__CX3CR1pos_CD45_1pos_CD8

source_name: spleen

value: spleen


title: 6C_S8


title: Horse 14, immune, d3pi

description:
NE21-Horse14-D3pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: A375_BRAF-T-3_R2


title: Horse 24, immune, d1pi

description:
NE16-Horse24-D1pi
ehv-1_rawCounts.txt


title: Horse 20, non-immune, d1pi

description:
NE15-Horse20-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: 6B_S6


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse9_liver

description:
CX3CR1pos_CD45_1pos_CD8_mouse9_liver
AdHBV_resolved__liver__CX3CR1pos_CD45_1pos_CD8

value: liver


title: A375_BRAF-T-3_R1

value: skin melanoma


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse8_liver

description:
CX3CR1pos_CD45_1pos_CD8_mouse8_liver
AdHBV_resolved__liver__CX3CR1pos_CD45_1pos_CD8


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse8_spleen

description:
CX3CR1pos_CD45_1pos_CD8_mouse8_spleen
AdHBV_resolved__spleen__CX3CR1pos_CD45_1pos_CD8


title: A375_BRAF-T-1_R3

value: MAPK inhibitors followed by tryptolide treatment for 1 hours


title: Horse 15, non-immune, d1pi

description:
NE14-Horse15-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt

value: nasal mucosa

value: EHV-1 Ab4 challenge


title: A375_BRAF-T-1_R2


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse7_spleen

description:
CX3CR1pos_CD45_1pos_CD8_mouse7_spleen
AdHBV_resolved__spleen__CX3CR1pos_CD45_1pos_CD8


title: Horse 11, immune, d1pi

description:
NE12-Horse11-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: 5D_S11

value: D1-expressing neuron


title: 7B_S1

value: female


title: Horse 14, immune, d1pi

description:
NE13-Horse14-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: 7A_S7


title: A375_BRAF-T-1_R1


title: 5C_S7


title: AdHBV_persistent_CXCR6pos_CD45_1pos_CD8_mouse11_liver

description:
CXCR6pos_CD45_1pos_CD8_mouse11_liver
AdHBV_persistent__liver__CXCR6pos_CD45_1pos_CD8

value: persistent AdHBV infection


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse7_liver

description:
CX3CR1pos_CD45_1pos_CD8_mouse7_liver
AdHBV_resolved__liver__CX3CR1pos_CD45_1pos_CD8

value: resolved AdHBV infection


title: Horse 6, immune, d1pi

description:
NE11-Horse6-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt

value: immune


title: 5A_S5


title: Horse 5, non-immune, d1pi

description:
NE10-Horse5-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt

value: Icelandic


title: A375_BRAF-T-0_R2

value: MAPK inhibitors followed by tryptolide treatment for 0 hours


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse6_liver

description:
CX3CR1pos_CD45_1pos_CD8_mouse6_liver
AdHBV_resolved__liver__CX3CR1pos_CD45_1pos_CD8


title: 6A_S6


title: 4D_S6


title: A375_BRAF-T-0_R1


title: 4C_S6


title: A375_BRAF-DMSO-5_R3

value: MAPK inhibitors followed by DMSO treatment for 5 hours


title: Horse 24, immune, d-2

description:
NE8-Horse24-Dm2pre
equine_rawCounts.txt


title: 4A_S4


title: Horse 20, non-immune, d-2

description:
NE7-Horse20-Dm2pre
equine_rawCounts.txt

value: non-immune


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse10_liver

description:
CX3CR1pos_CD45_1pos_CD8_mouse10_liver
AdHBV_resolved__liver__CX3CR1pos_CD45_1pos_CD8


title: A375_BRAF-DMSO-5_R2


title: Horse 15, non-immune, d-2

description:
NE6-Horse15-Dm2Pre
equine_rawCounts.txt


title: A375_BRAF-DMSO-3_R3

value: MAPK inhibitors followed by DMSO treatment for 3 hours


title: 3B_S3

value: male


title: Horse 14, immune, d-2

description:
NE5-Horse14-Dm2Pre
equine_rawCounts.txt


title: A375_BRAF-T-0_R3


title: 3C_S5


title: Horse 11, immune, d-2

description:
NE4-Horse11-Dm2Pre
equine_rawCounts.txt


title: A375_BRAF-DMSO-5_R1


title: Horse 3, non-immune, d1pi

description:
NE9-Horse3-D1pi
equine_rawCounts.txt
ehv-1_rawCounts.txt


title: AdHBV_resolved_CD45_1neg_CD8_mouse8_liver

description:
CD45_1neg_CD8_mouse8_liver
AdHBV_resolved__liver__CD45_1neg_CD8


title: 3A_S3


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse10_spleen

description:
CX3CR1pos_CD45_1pos_CD8_mouse10_spleen
AdHBV_resolved__spleen__CX3CR1pos_CD45_1pos_CD8

value: spleen


title: AdHBV_resolved_CD45_1neg_CD8_mouse8_spleen

description:
CD45_1neg_CD8_mouse8_spleen
AdHBV_resolved__spleen__CD45_1neg_CD8


title: Horse 6, immune, d-2

description:
NE3-Horse6-Dm2Pre
equine_rawCounts.txt


title: 2D_S4


title: A375_BRAF-DMSO-3_R1


title: AdHBV_resolved_CD45_1neg_CD8_mouse9_spleen

description:
CD45_1neg_CD8_mouse9_spleen
AdHBV_resolved__spleen__CD45_1neg_CD8


title: AdHBV_resolved_CX3CR1pos_CD45_1pos_CD8_mouse6_spleen

description:
CX3CR1pos_CD45_1pos_CD8_mouse6_spleen
AdHBV_resolved__spleen__CX3CR1pos_CD45_1pos_CD8


title: AdHBV_resolved_CD45_1neg_CD8_mouse7_spleen

description:
CD45_1neg_CD8_mouse7_spleen
AdHBV_resolved__spleen__CD45_1neg_CD8


title: 2C_S4


title: AdHBV_resolved_CD45_1neg_CD8_mouse7_liver

description:
CD45_1neg_CD8_mouse7_liver
AdHBV_resolved__liver__CD45_1neg_CD8

value: liver


title: H9-PE, dRNA-ONT

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

description: Direct RNA sequencing (SQK-DCS109 Kit) for Library prepration; R9.4.1 flow cell for sequencing

data_processing:
For ONT long-read RNA-seq, only the long reads with a quality score (qscore ≥7, passed reads) are used for our study, and these passed reads are uploaded to NCBI GEO.  For Illumina short-read RNA-seq, sequencing adapters are trimmed by Cutadapt (v1.8.1)  with the parameter “-q 20,20 -m 20 --max-n 0.01 --trim-n”.
ReDD (v1.0.0) with sample-specific model is run separately on the ONT direct RNA seq data to obtain the A-to-I editing sites and editing level.
REDItools2 (v2.0.0) is run on the Illumina RNA-seq data to obtain the A-to-I editing sites and editing level.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by ReDD.
Supplementary files format and content: Tab-delimited text files included the A-to-I editing sites and the editing level of the sites by REDItools2.

growth_protocol: Definitive endoderm (DE) and pharyngeal endoderm (PE), and primordial germ cell-like cells (PGC) (reference: PMID: 37709760) are differentiated from human ESC (H1-hESC cell line), respectively. See the details in the manuscripts: (1)  DOI: https://doi.org/10.1101/2022.06.26.497457 (from ESC to DE and PE); and (2) PMID: 37709760 (from ESC to PGC).

extract_protocol:
Total RNA is extracted by TRIzol Reagent (Thermo Fisher Scientific), followed by polyA+ RNA enrichment using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific).
For H1-ESC, H1-PE, H1-DE, H1-PGC,H9-hESC,H9-PE,H9-DE and HEK293T, ONT sequencing libraries are prepared using the SQK-DCS109 Kit for direct RNA sequencing (dRNA-ONT). ONT sequencing is conducted using MiniON/GridION flow cells with R9.4.1 chemistry, with real-time base calling performed by the Guppy software. The library preparation and sequencing of Illumina RNA-seq data are conducted by Novogene company.

value: H9-hESC derived pharyngeal endoderm


title: 3D_S5


title: AdHBV_resolved_CD45_1neg_CD8_mouse9_liver

description:
CD45_1neg_CD8_mouse9_liver
AdHBV_resolved__liver__CD45_1neg_CD8


title: AdHBV_resolved_CD45_1neg_CD8_mouse6_spleen

description:
CD45_1neg_CD8_mouse6_spleen
AdHBV_resolved__spleen__CD45_1neg_CD8


title: A375_BRAF-DMSO-1_R2

value: skin melanoma

value: MAPK inhibitors followed by DMSO treatment for 1 hours


title: A375_BRAF-DMSO-3_R2


title: H9-DE, dRNA-ONT

value: H9-hESC derived definitive endoderm


title: A375_BRAF-DMSO-1_R1


title: AdHBV_resolved_CD45_1neg_CD8_mouse6_liver

description:
CD45_1neg_CD8_mouse6_liver
AdHBV_resolved__liver__CD45_1neg_CD8


title: A375_BRAF-DMSO-0_R3

value: MAPK inhibitors followed by DMSO treatment for 0 hours


title: H9-hESC, dRNA-ONT

value: H9 human embryonic stem cells


title: 24D_S12

source_name: D2-expressing neuron

value: D2-expressing neuron

value: female


title: AdHBV_persistent_CD45_1neg_CD8_mouse15_liver

description:
CD45_1neg_CD8_mouse15_liver
AdHBV_persistent__liver__CD45_1neg_CD8

value: persistent AdHBV infection


title: Horse 5, non-immune, d-2

description:
NE2-Horse5-Dm2Pre
equine_rawCounts.txt

value: nasal mucosa

value: EHV-1 Ab4 challenge

value: Icelandic


title: AdHBV_persistent_CD45_1neg_CD8_mouse14_liver

description:
CD45_1neg_CD8_mouse14_liver
AdHBV_persistent__liver__CD45_1neg_CD8


title: H1-PGC, dRNA-ONT

value: H1-hESC derived primordial germ cell-like cells


title: A375_BRAF-DMSO-0_R2


title: A375_BRAF-DMSO-1_R3


title: AdHBV_persistent_CD45_1neg_CD8_mouse13_liver

description:
CD45_1neg_CD8_mouse13_liver
AdHBV_persistent__liver__CD45_1neg_CD8


title: H1-PE, dRNA-ONT

value: H1-hESC derived pharyngeal endoderm


title: 24B_S2


title: A375_BRAF-CHX-5_R3

value: MAPK inhibitors followed by cycloheximid treatment for 5 hours


title: 2B_S2

value: D1-expressing neuron

value: male


title: 24A_S12


title: H1-DE, dRNA-ONT

value: H1-hESC derived definitive endoderm


title: A375_BRAF-CHX-5_R2

value: skin melanoma


title: HEK293T_dMut, dRNA-ONT

value: human epithelial like cells


title: H1-hESC, dRNA-ONT

value: H1 human embryonic stem cells


title: 23D_S12


title: AdHBV_persistent_CD45_1neg_CD8_mouse11_liver

description:
CD45_1neg_CD8_mouse11_liver
AdHBV_persistent__liver__CD45_1neg_CD8

value: liver


title: AdHBV_resolved_CD45_1neg_CD8_mouse10_spleen

description:
CD45_1neg_CD8_mouse10_spleen
AdHBV_resolved__spleen__CD45_1neg_CD8

value: spleen

value: resolved AdHBV infection


title: 23C_S1

value: D2-expressing neuron

value: female


title: HEK293T_WT, dRNA-ONT


title: 2A_S2


title: 24C_S2


title: A375_BRAF-CHX-3_R3

value: MAPK inhibitors followed by cycloheximid treatment for 3 hours


title: 23B_S1


title: A375_BRAF-DMSO-0_R1

value: MAPK inhibitors followed by DMSO treatment for 0 hours


title: MPP2-4OHT

city: Tsu

first: Ryoichi

last: Ono

address: 2-174 Edobashi

department: Department of Microbiology

country: Japan

institute: Mie University Graduate School of Medicine

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.36.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: MPP2 cells

growth_protocol: ST-HSCs and MPP2 cells (100 cells) were cultured in 1ml of 1% methylcellulose medium  supplemented with 25 ng/ml of SCF, 10 ng/ml each of IL-6, IL-3, and GM-CSF, in the presence of 4OHT or ethanol for 5-7 days.

extract_protocol:
Total RNA samples were extracted from colony-forming cells with TRI Reagent LS (Molecular Research Center, Inc.), followed by purification using RNeasy Mini Kit (QIAGEN).
The sequencing libraries were prepared from 200 ng of total RNA with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions.

treatment_protocol: In the medium, 0.05 μM of 4-hydroxytamoxifen (4OHT) dissolved in ethanol (EtOH) or an equal amount of ethanol as a vehicle control was added.

value: MPP2 cells

tag: conditional expression

value: MLL-ENL


title: 23A_S11


title: MPP2-EtOH

value: EtOH

value: control


title: AL5852_d4_siPRRX1_N3

data_processing:
Reads were aligned to CanFam3.1 genome annotation (Ensembl v97) using STAR (2.5.3a)
Quality control of sequenced reads was performed using FastQC (Babraham Institute)
Gene expression was quantified using RSEM (1.3.0)
Genome_build: CanFam3.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: MDCK-NBL2 cell line

growth_protocol: Detailed protocol available in the material and methods part from Youssef et al. 2021

extract_protocol:
illustra RNAspin  (GE Healthcare)
mRNA (stranded)

value: Madin-Darby Canine Kidney (MDCK) cells

value: TGFb (5mg/ml) + siPRRX1

value: 4 days

tag: replicate

tag: description (phenotype)

value: partial EMT


title: A375_BRAF-CHX-3_R2

value: skin melanoma


title: AdHBV_resolved_CD45_1neg_CD8_mouse10_liver

description:
CD45_1neg_CD8_mouse10_liver
AdHBV_resolved__liver__CD45_1neg_CD8


title: AL2683_d4_TGFb_N3

treatment_protocol: Detailed protocol available in the material and methods part from Youssef et al. 2021

value: TGFb (5mg/ml)

value: full EMT


title: AdHBV_persistent_CD45_1neg_CD8_mouse12_liver

description:
CD45_1neg_CD8_mouse12_liver
AdHBV_persistent__liver__CD45_1neg_CD8

value: liver

value: persistent AdHBV infection


title: A375_BRAF-CHX-3_R1


title: AL5851_d4_siCTR_N3

value: TGFb (5mg/ml) + siCTR


title: ST-4OHT

source_name: ST-HSCs

value: ST-HSCs


title: A375_BRAF-CHX-5_R1

value: MAPK inhibitors followed by cycloheximid treatment for 5 hours


title: A375_BRAF-CHX-1_R3

value: MAPK inhibitors followed by cycloheximid treatment for 1 hours


title: 22D_S11

value: D2-expressing neuron

value: female


title: Bil_system_R2

city: Rehovot

first: Jens

last: Hör

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute for Science

data_processing:
Demultiplexing using bcl-convert v4.2.4
Trimming using Trim Galore v0.6.7 with default parameters
Mapping using BBMap v39.06 with default parameters
Read counting using featureCounts v2.0.3 with -s 1
Assembly: GCF_001425745.1, NC_000913.3
Supplementary files format and content: Excel file containing TPM values for each sample

organism: Escherichia coli

extract_protocol:
E. coli expressing the Bil system under control of a tetracycline-inducible promoter was grown to mid-log phase with 25 ng/ml aTc as inducer. Caulobacter sp. Root343 was grown to mid-log, late-log or early stationary phase. Samples corresponding to an OD600 of 2 were taken and immediately mixed with ¼ volume of stop mix (95% ethanol, 5% saturated phenol) and frozen in liquid nitrogen. The samples were then thawed on iced followed by centrifugation at 4,000 g and 4°C for 10 min. The supernatant was discarded and the cell pellets resuspended in 1 ml of TRIzol (Thermo Scientific) followed by RNA extraction according to the manufacturer’s protocol. The resulting RNA pellet was dissolved in 40 µl of water. To get rid of contaminating DNA, 0.5 µl of water, 5 µl DNase I buffer with MgCl2 (Thermo Scientific), 0.5 µl of RNase inhibitor (Thermo Scientific) and 4 µl DNase I (Thermo Scientific) was added and the mixture incubated at 37°C for 30 min. The DNase-digested RNA was subjected to acidic phenol-chloroform extraction and finally dissolved in 30 µl of water.
Extracted RNA was depleted of ribosomal RNA using a commercial rRNA depletion kit for mixed bacterial samples (Lexogen, RiboCop META, #125). The depleted RNA samples were fragmented using ultrasound (2 pulses of 30 s at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase with the 3’ adapter as primer. After purification, the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified using a high-fidelity DNA polymerase and the barcoded TruSeq-libraries were pooled in approximately equimolar amounts. Sequencing of pooled libraries, spiked with PhiX control library, was performed at a minimum of 10 million reads per sample in single-ended mode with 100 cycles on the NextSeq 2000 platform (Illumina).


title: AL2681_d0_N3

value: Untreated

value: 0 days

value: epithelial


title: 21D_S10


title: 22C_S12


title: A375_BRAF-CHX-1_R1


title: A375_BRAF-CHX-0_R3

value: MAPK inhibitors followed by cycloheximid treatment for 0 hours


title: Bil_system_R1


title: AL5855_d4_siPRRX1_N2

value: Madin-Darby Canine Kidney (MDCK) cells

value: TGFb (5mg/ml) + siPRRX1

value: 4 days


title: ST-EtOH

value: EtOH

value: control


title: 22B_S12


title: A375_BRAF-CHX-1_R2

value: skin melanoma


title: AL2682_d4_UN_N3


title: 22A_S10


title: Bil_system_R3


title: A375_BRAF-CHX-0_R1


title: NTG Meninges female bio rep2

type: RNA

city: Chapel Hill

first: Nathan

last: Nelson-Maney

state: North Carolina

address: 111 mason farm road

department: Cell Biology and Physiology

institute: UNC Chapel Hill

description: Ribosome bound mRNA from Lyve1+ Meningeal lymphatic endothelial cells from dorsal meningeal tissue from female Lvye1 Cre RiboTag mice, Treated with NTG

hyb_protocol: The GeneChip™ Hybridization, Wash, and Stain Kit was used to prepare the ds-cDNA samples for hybridization. Fragmented and labeled ds-cDNA was added to a hybridization cocktail (50 ng/µl fragmented and labeled ds-cDNA final concentration, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 7 % DMSO, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20).  Thermo Fisher Clariom S Mouse arrays were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 645 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader. GeneChip Command Console Software (AGCC) was used for washing, staining and scanning control of the instrumentation

data_processing:
Transcriptome Analysis Console Software v 4.0 was used for basic data analysis and quality control. Signal intensity was generated using SST-RMA algorithm. Biological level data analysis was performed using Partek Genome Suite software. Gene level expression were summarized from the corrected intensities and then quantile normalized prior to secondary analysis.
Quantile normalized gene level expression values from GeneBASE

label: biotin

label_protocol: Total RNA (10 ng) was used to synthesize fragmented and labeled double-stranded cDNA (ds-cDNA) and hybridized onto Thermo Fisher arrays. The Thermo Fisher® GeneChip™ 3’ IVT Pico Kit Manual Workflow User Guide was followed to prepare the samples. Briefly, the GeneChip™ Pico Kit (Thermo Fisher) was used to generate ds-cDNA from total RNA. Following synthesis of ds-cDNA, the cDNA is converted to biotinylated ds-cDNA hybridization targets for unbiased coverage of the transcriptome.

growth_protocol: meninges dissected from 3 month old mice

extract_protocol: whole tissue was lysed using Lysing Matrix D beads. Hemagglutinin positive Ribosomes were immunoprecipitated using anti-HA conjugated magnetic beads. RNA was extracted using Qiagen RNeasy Kit. See methods for additional information

treatment_protocol: mice were treated with either 10 mg/kg NTG or vehicle every other day for 9 days, for 5 total injections. Mice were euthanized 60 minutes after the final injection.

value: Chronic NTG

value: 3 months


title: NTG Meninges female bio rep3

source_name: Lyve1+ Meningeal lymphatic endothelial cells


title: 21C_S11


title: AL5854_d4_siCTR_N2

value: TGFb (5mg/ml) + siCTR

value: full EMT


title: A375_BRAF-CHX-0_R2


title: 21B_S11


title: A375_DMSO-0D_R3

data_processing:
Adapters were removed from raw reads and trimmed using fastp version 0.20.1 (parameters --qualified_quality_phred 30 -l 25 --detect_adapter_for_pe)
Reads were mapped against the human genome GRCh38.p13 with hisat2 version 2.2.1
Reads were counted with htseq-count version 0.13.5. (parameters -r pos -a 10 -s reverse -t exon).
Assembly: GRCH38.p13
Supplementary files format and content: tab-delimited text file containing raw read counts for each sample. (readcounts_raw_44659genes.csv)

extract_protocol:
Cells were washed twice with ice cold PBS, then scrapped with 1ml of PBS. Then they were centrifuged (500g for 1min at 4°C) and slowly resuspended in 1ml of lysis buffer (10mM Tris-HCL pH7.5; 5mM MgCl2; 100 mM KCl; 1% Triton X-100), and incubated on ice for 10 minutes. After this, lysates were centrifuged (1000g for 10minutes at 4°C), and RNAs were extracted from cytoplasmic fractions using tri-reagent (Sigma, T9424) following the manufacturer’s instructions.
RNA samples were sent for sequencing at Novogene (rRNA depletion library preparations, sequencing on Novaseq 6000 2x150)

treatment_protocol: Cells were plated and the following day, the culture medium was removed and replaced with fresh medium containing 1µM vemurafenib and cobimetinib (500nM vemurafenib + 500nM cobimetinib) or DMSO, in 3 identical batches A B C. 3 days after treatment, batch A cells were harvested (D0 samples), and batches B and C cells were washed with warm PBS and had their medium replaced with fresh drug-free DMEM for recovery. 2 days after this, batch B cells were harvested (D2 samples), while batch C cells were harvested after 9 days of recovering (D9 samples). Cells were passed when necessary during this process.

value: cells treated for 72h with DMSO


title: 21A_S13

value: D2-expressing neuron


title: AL2674_d4_UN_N2

value: Untretaed


title: A375_DMSO-0D_R2


title: 20D_S9

value: female


title: VEH Meninges female bio rep3

description: Ribosome bound mRNA from Lyve1+ Meningeal lymphatic endothelial cells from dorsal meningeal tissue from female Lvye1 Cre RiboTag mice, treated with vehicle

value: Vehicle


title: AL2673_d0_N2

value: Untreated

value: 0 days

value: epithelial


title: 20C_S10


title: AL2669_d4_siPRRX1_N1

value: Madin-Darby Canine Kidney (MDCK) cells

value: TGFb (5mg/ml) + siPRRX1

value: partial EMT


title: NTG Meninges female bio rep1

value: Lyve1+ Meningeal lymphatic endothelial cells


title: A375_MAPKi-9D_R3

value: skin melanoma

value: cells treated for 72h with MAPKi and recovered 9 days in drug-free medium


title: VEH Meninges female bio rep2

value: 3 months


title: VEH Meninges female bio rep1


title: A375_DMSO-0D_R1


title: AL2668_d4_siCTR_N1

value: TGFb (5mg/ml) + siCTR

value: 4 days


title: 20A_S8


title: A375_MAPKi-9D_R2


title: AL5853_d4_TGFb_N1

value: TGFb (5mg/ml)

value: full EMT


title: 1D_S3

value: D1-expressing neuron

value: male


title: A375_MAPKi-9D_R1


title: A375_MAPKi-2D_R3

value: cells treated for 72h with MAPKi and recovered 2 days in drug-free medium


title: 1C_S3


title: A375_MAPKi-2D_R2


title: AL2680_d4_TGFB_N3

source_name: MDCK-II cell line

value: MDCK-II


title: AL2650_d4_UN_N1

value: Untreated


title: AL2649_d0_UN_N1

value: 0 days

value: epithelial


title: 1A_S1


title: AL2679_d4_UN_N3

value: Madin-Darby Canine Kidney (MDCK) cells


title: A375_MAPKi-2D_R1


title: AL2678_d0_N3


title: 20B_S10

value: D2-expressing neuron

value: female


title: 19D_S8


title: Serum sample of highly myopic patient IgM 26

type: protein

city: Shanghai

first: Xiangjia

last: Zhu

address: No.83 Fenyang Road

institute: Eye & ENT Hospital, Fudan University

description: IgM

hyb_protocol: After blocking 1h, HuProt array was incubated in 3 ml 1:1,000 diluted serum sample to capture corresponding autoantibodies to each protein spot, and followed with 1:2,000 diluted Cy3-conjugated goat anti-human IgG (Jackson, 109-165-008) and Alexa Fluor 647-affinipure donkey anti-human IgM (Jackson, 709-605-073) to fluorescently label IgG and IgM of captured autoantibodies, respectively.

scan_protocol: Scanned using the GenePix 4000B Microarray Scanner (Molecular Devices, Sunnyvale, CA, USA) and analyzed with GenePix Pro 6.0 software (Molecular Devices, Sunnyvale, CA, USA)

data_processing: The signal intensity of each protein spot was calculated as the ratio of foreground to background signal intensity. Each protein was duplicated in pairs, thus, the signal intensity of each autoantibody was calculated as the mean of both protein spots.

molecule: protein

source_name: High myopia

extract_protocol: 1 ml venous blood per subject was collected into a promoting coagulant vacuum blood tube. The top layer serum samples after centrifugation at 3000 rpm for 10 min at 4 °C within 4 h after collection were sucked out and stored at −80 °C until use.

value: Sera

tag: molecular

value: Autoantibody

tag: age (years)

value: Female

tag: al


title: 19C_S9

tag: time


title: Serum sample of highly myopic patient IgM 25

description: IgM

label_protocol: 1:2,000 diluted Cy3-conjugated goat anti-human IgG (Jackson, 109-165-008) and Alexa Fluor 647-affinipure donkey anti-human IgM (Jackson, 709-605-073) to fluorescently label IgG and IgM

tag: tissue


title: AL2672_d4_TGFb_N2

tag: treatment

value: partial EMT


title: A375_MAPKi-0D_R2

tag: cell type

value: skin melanoma

value: cells treated for 72h with MAPKi


title: A375_MAPKi-0D_R1


title: AL2671_d4_UN_N2

value: 4 days


title: 19A_S7


title: Serum sample of highly myopic patient IgM 24

description: IgM

value: Male


title: HMEC-1 CPPs-Exo 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genomes for rat or human using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Genome Reference Consortium GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HMEC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
HMEC-1 cells were digestion with trypsin, terminated with DMEM supplemented with 10% FBS, and then washed with PBS.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HMEC-1 cells were treated with or without exosomes from cardiopulmonary progenitors for 48 hours.

value: endothelial cells

tag: genotype

value: WT

value: treated by exosomes from cardiopulmonary progenitors


title: 18D_S7

value: male


title: AL2670_d0_N2

tag: cell line

value: MDCK-II

value: Untreated

value: 0 days


title: Serum sample of highly myopic patient IgM 20

description: IgM


title: A375_MAPKi-0D_R3


title: HMEC-1 CPPs-Exo 2


title: 18C_S8

value: D2-expressing neuron


title: AL2648_d4_TGFb_N1

value: Madin-Darby Canine Kidney (MDCK) cells

value: TGFb (5mg/ml)


title: HMEC-1 CPPs-Exo 1


title: 18B_S9


title: HMEC-1 Control 3

value: without treated by exosomes from cardiopulmonary progenitors


title: AL2647_d4_UN_N1

value: epithelial


title: Serum sample of highly myopic patient IgM 21

description: IgM

value: Sera

value: Autoantibody

value: Female


title: Serum sample of highly myopic patient IgM 23

description: IgM


title: 18A_S6


title: AL2646_d0_N1


title: HMEC-1 Control 2


title: 17D_S6


title: Serum sample of highly myopic patient IgM 22

description: IgM


title: Serum sample of highly myopic patient IgM 17

description: IgM


title: 17C_S7


title: Serum sample of highly myopic patient IgM 19

description: IgM


title: Serum sample of highly myopic patient IgM 15

description: IgM


title: HMEC-1 Control 1


title: Serum sample of highly myopic patient IgM 18

description: IgM


title: A375_-Q_R3 [Q_230]

treatment_protocol: For the MAPKi experiment : cells were plated and the following day, the culture medium was removed and replaced with fresh medium containing 1µM MAPK inhibitors (500nM vemurafenib + 500nM cobimetinib) and cells were cultured for 24h before harvesting.  For the glutamine depletion experiment : cells were plated and the following day, the culture medium was removed, cells were washed with warm PBS and put in a fresh glutamine-free medium, and cells were cultured for 24h before harvesting.

value: skin melanoma

value: Q depleted medium for 24h

tag: molecule subtype

value: cytoplasmic RNA

tag: batch

value: sequencing batch #1 - experimental batch 2


title: AL2675_d4_TGFb_N2

value: 4 days

value: full EMT


title: 17B_S8

tag: Sex

value: male


title: A375_-Q_R2 [Q_226]


title: Time Point_7dpc_Group_PBS_Sample19

city: Bellaterra

first: Jordi

last: Argilaguet Marqués

state: Barcelona

address: CAMPUS UAB EDIF.CRESA

institute: IRTA-CReSA

data_processing:
Reads mapped with STAR v2.7.8a
Genes quantified with RSEM v1.3.0
Assembly: Concatenation of Sscrofa11.1 and KP055815
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

organism: Sus scrofa domesticus

source_name: Whole Blood

extract_protocol:
Phenol-chloroform method, and further purified using RNeasy mini Kit, QIAGEN (RNAse-free water) following the manufacturer’s protocol. DNase I (RNase-Free DNase Set, Qiagen) treatment for 15 min at room temperature was performed to ensure RNA quality. Total RNA from whole blood was submitted for sequencing to the Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain. Total RNA was quantified by Qubit RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNASeq libraries were prepared with KAPA mRNA HyperPrep Kit (Roche) following the manufacturer´s recommendations starting with 500 ng of total RNA as the input material. The library was quality controlled on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on NovaSeq 6000 (Illumina) with a read length of 2x51bp, following the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4).

treatment_protocol: Whole blood was kept at -80˚C in TRIzol Reagent (Invitrogen) until use.

tag: age

value: 27 weeks old

tag: diet

value: ad libitum

value: Whole Blood

value: primary

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 7 days post-challenge

value: Challenge


title: Time Point_7dpc_Group_PBS_Sample20


title: Time Point_7dpc_Group_PBS_Sample18


title: Serum sample of highly myopic patient IgM 14

description: IgM

value: Sera


title: Time Point_7dpc_Group_PBS_Sample17


title: Time Point_7dpc_Group_PBS_Sample16


title: 16D_S5

value: D2-expressing neuron


title: Serum sample of highly myopic patient IgM 16

description: IgM

value: Autoantibody

value: Female


title: A375_-Q_R1 [Q_185]

value: skin melanoma

value: Q depleted medium for 24h

value: sequencing batch #1 - experimental batch 1


title: Time Point_7dpc_Group_3dv_Sample15

value: Vaccination and challenge


title: A375_CTRL_R3 [CTRL_230]

value: control medium for 24h

value: cytoplasmic RNA

value: sequencing batch #1 - experimental batch 2


title: 16C_S6

value: male


title: Serum sample of highly myopic patient IgM 13

description: IgM


title: Serum sample of highly myopic patient IgM 12

description: IgM

value: Male


title: A375_CTRL_R2 [CTRL_226]


title: 16B_S7


title: Time Point_7dpc_Group_3dv_Sample13

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: primary


title: A375_CTRL_R1 [CTRL_185]


title: 16A_S4


title: Time Point_7dpc_Group_3dv_Sample14

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 7 days post-challenge


title: Serum sample of highly myopic patient IgM 10

description: IgM

value: Sera

value: Autoantibody


title: A375_DMSO_R3 [DMSO_247]

value: skin melanoma

value: DMSO for 24h

value: sequencing batch #2


title: Serum sample of highly myopic patient IgM 11

description: IgM

value: Female


title: 17A_S5

value: D2-expressing neuron


title: 15D_S4


title: Serum sample of highly myopic patient IgM 9

description: IgM


title: Time Point_7dpc_Group_3dv_Sample12

value: Vaccination and challenge


title: A375_DMSO_R2 [DMSO_246]

value: cytoplasmic RNA


title: 15C_S5

value: male


title: Time Point_7dpc_Group_3dv_Sample11


title: A375_DMSO_R1 [DMSO_245]


title: Serum sample of highly myopic patient IgM 7

description: IgM


title: Time Point_7dpc_Group_7dv_Sample10


title: 15A_S3


title: A375_MAPKi_R3 [BRAF_247]

value: MAPK inhibitors for 24h


title: Time Point_7dpc_Group_7dv_Sample9

value: 27 weeks old


title: A375_MAPKi_R2 [BRAF_246]


title: 15B_S6


title: 14D_S3


title: Time Point_7dpc_Group_7dv_Sample8

value: ad libitum


title: Serum sample of highly myopic patient IgM 6

description: IgM


title: Time Point_7dpc_Group_7dv_Sample7

value: Whole Blood


title: A375_MAPKi_R1 [BRAF_245]


title: 14C_S4


title: Serum sample of highly myopic patient IgM 5

description: IgM

value: Male


title: KFO-24

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0.422
STAR version 2.7.8a was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 107
Assembly: hg38 gene version 107
Supplementary files format and content: Tab-delimited gene counts

source_name: primary pancreatic ductal adenocarcinoma (PDAC)

extract_protocol:
ReliaPrep™ FFPE Total RNA Miniprep System (Promega)
TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat (Cat. N°20020596)


title: 14A_S2


title: KFO-23

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: 13D_S2


title: Serum sample of highly myopic patient IgM 8

description: IgM


title: Time Point_7dpc_Group_7dv_Sample6

value: primary

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 7 days post-challenge


title: Serum sample of highly myopic patient IgM 2

description: IgM

value: Sera

value: Autoantibody


title: Time Point_7dpc_Group_12dv_Sample5


title: 13C_S3


title: Time Point_7dpc_Group_12dv_Sample4


title: Serum sample of highly myopic patient IgM 3

description: IgM


title: Serum sample of highly myopic patient IgM 1

description: IgM


title: 13B_S8


title: 13A_S1


title: Time Point_7dpc_Group_12dv_Sample2


title: Serum sample of emmetropic control IgM 8

description: IgM

source_name: Emmetropia


title: Serum sample of emmetropic control IgM 7

description: IgM


title: Serum sample of highly myopic patient IgM 4

description: IgM


title: 12C_S2

value: D1-expressing neuron

value: female


title: KFO-18


title: Time Point_3dpc_Group_PBS_Sample20

value: 3 days post-challenge

value: Challenge


title: Serum sample of emmetropic control IgM 10

description: IgM

value: Female


title: KFO-22


title: Time Point_7dpc_Group_12dv_Sample3

value: Vaccination and challenge


title: 12B_S5


title: KFO-17


title: Serum sample of emmetropic control IgM 6

description: IgM


title: Time Point_3dpc_Group_PBS_Sample19


title: KFO-21


title: KFO-16


title: Serum sample of emmetropic control IgM 5

description: IgM


title: 12A_S12


title: Time Point_3dpc_Group_PBS_Sample18


title: KFO-15


title: 11D_S12


title: Time Point_3dpc_Group_PBS_Sample17


title: Time Point_7dpc_Group_12dv_Sample1


title: KFO-14


title: 11C_S1


title: 11A_S11


title: Time Point_3dpc_Group_PBS_Sample16


title: KFO-13


title: Serum sample of emmetropic control IgM 1

description: IgM


title: Time Point_3dpc_Group_3dv_Sample15


title: KFO-12


title: Time Point_3dpc_Group_3dv_Sample14


title: KFO-11


title: Time Point_3dpc_Group_3dv_Sample13


title: 10C_S12


title: 10D_S11


title: Serum sample of emmetropic control IgM 3

description: IgM


title: KFO-10


title: Serum sample of highly myopic patient IgG 26

description: IgG


title: Serum sample of highly myopic patient IgG 25

description: IgG


title: Time Point_3dpc_Group_3dv_Sample12


title: 10B_S4


title: Serum sample of emmetropic control IgM 2

description: IgM


title: Serum sample of highly myopic patient IgG 24

description: IgG


title: Time Point_3dpc_Group_7dv_Sample10


title: KFO-9


title: 10A_S10


title: 1B_S1

value: male


title: Serum sample of highly myopic patient IgG 23

description: IgG


title: W10_5_R1_P

city: Laval

first: Isabelle

last: Plante

state: Québec

address: 531 boul Des prairies

department: Armand-Frappier Santé Biotechnologie

country: Canada

institute: INRS

description: miRNA

data_processing:
Trimming the adaptor residues and low quality regions: a. Application: trimmomatic/0.36 (Bolger, 2014) b. Options: SE, ILLUMINACLIP: adapters.fa:2:30:5, SLIDINGWINDOW:5:20, MINLEN:18
Quality control: fastQC (Andrews, 2010), MultiQC (Ewels, 2016)
Mapping the reads against the reference genome a. Application: QuickMirSeq (Zhao, 2017) b. Databse : miRBase/22 (Kozomara, 2019) c. Options : a. CUTADAPT_PARAMETER="-a AGATCGGAAGAG -m 18" b. OFFSET_ANALYSIS=yes c. MIN_MIRNA_LENGTH=18 d. MAX_MIRNA_LENGTH=36 e. ZEROCOUNT_THRESHOLD=0 f. ZEROCOUNT_SAMPLE_THRESHOLD=0.60 g. AVG_READ_THRESHOLD=2 h. SPECIES=mouse i. Reference genome: Mus_musculus.GRCm38
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: miR_normalized_counts, CSV Microsoft Excel File

source_name: mammary gland

extract_protocol:
mirVana miRNA isolation kit (Thermo Fisher Scientific).
Qiaseq miRNA

value: mammary gland

value: C57/BL6 female

value: 10 week old mice


title: Serum sample of highly myopic patient IgG 22

description: IgG


title: Time Point_3dpc_Group_3dv_Sample11

value: 27 weeks old

value: ad libitum

value: Whole Blood


title: KFO-6

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: W10_7_R1_P

description: miRNA


title: KFO-5


title: Time Point_3dpc_Group_7dv_Sample9

value: primary

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: KFO-7


title: Time Point_3dpc_Group_7dv_Sample8


title: Serum sample of highly myopic patient IgG 20

description: IgG

value: Sera

value: Autoantibody

value: Male


title: KFO-19


title: Serum sample of highly myopic patient IgG 19

description: IgG


title: W10_3_R1_P

description: miRNA


title: KFO-4


title: W10_4_R1_P

description: miRNA


title: KFO-8


title: W10_2_R1_P

description: miRNA


title: Serum sample of highly myopic patient IgG 18

description: IgG


title: Time Point_3dpc_Group_7dv_Sample6

value: 3 days post-challenge


title: Time Point_3dpc_Group_7dv_Sample7


title: KFO-3


title: Time Point_3dpc_Group_12dv_Sample5


title: W10_1_R1_P

description: miRNA


title: Time Point_3dpc_Group_12dv_Sample3


title: KFO-1


title: P18_5_R1_P

description: miRNA

value: pregnancy day 18


title: Serum sample of highly myopic patient IgG 21

description: IgG

value: Female


title: Serum sample of highly myopic patient IgG 16

description: IgG


title: P18_6_R1_P

description: miRNA


title: KFO-2


title: P18_4_R1_P

description: miRNA


title: Serum sample of highly myopic patient IgG 15

description: IgG


title: Time Point_3dpc_Group_12dv_Sample4

value: Vaccination and challenge


title: P18_3_R1_P

description: miRNA


title: Time Point_3dpc_Group_12dv_Sample1


title: Serum sample of highly myopic patient IgG 13

description: IgG


title: Time Point_3dpc_Group_12dv_Sample2


title: Serum sample of highly myopic patient IgG 17

description: IgG


title: Time Point_0dpc_Group_PBS_Sample19

value: 0 days post-challenge

value: Untreated


title: Pt-06 (GoT-ChA-ASAP) [Genotyping GoT-ChA amplicon]

city: New York

first: Franco

last: Izzo

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Genotyping GoT-ChA amplicon

data_processing:
FASTQ files were processed through the cell-ranger-atac (v2.0.0). Single cell ATAC-seq metadata files were generated by analysis with ArchR (v1.0.0),  Gotcha (v1.0.0) and GotchaMito (v1.0.0)
Assembly: hg38
Supplementary files format and content: Metadata including cell cluster and genotype assignments is available as .csv files.

source_name: Peripheral blood mononuclear cells (PBMC)

growth_protocol: Human CA46 (ATCC, #CRL-1648), HEL (ATCC, #TIB-180), SET-2 (DSMZ, #ACC 608) and CCRF-CEM (ATCC, #CRM-CCL-119) cell lines were maintained according to standard procedures in RPMI-1640 (Thermo Fisher Scientific, #11-875-119) with 10% (or 20% for CA46 and SET-2 cells) FBS (Thermo Fisher Scientific, #10-437-028) at 37˚C with 5% CO2. Cell lines in culture were screened biweekly for mycoplasma contamination using the MycoAlert PLUS Mycoplasma Detection Kit (Lonza, #LT07-703).

extract_protocol:
Patient samples were FACS-sorted using CD34+ DAPI- gating. Downstream processing using the 10X Chromium Solution platform for single cell ATAC sequencing, with the modifications of the GoT-ChA protocol.
Nuclei were subsequently processed according to the Chromium Next GEM Single Cell ATAC Solution user guide (version CG000209 Rev F, 10x Genomics) with the following modifications: 1- During the GEM Generation and Barcoding reaction (Step 2.1), 1 μL of 22.5 μM GoT-ChA primer mix was added to the barcoding reaction mixture. The primers used are GoT-ChA_R1N (locus-specific primer with a Read 1N handle sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG - [22bp locus specific]) and GoT-ChA_IS2 (locus- specific primer with an IS2 handle sequence: AGCAAGTGAGAAGCATCGTGTC - [22bp locus specific]). These primers allow for exponential amplification of the GoT-ChA fragments, relative to the linear amplification of ATAC fragments. 2- During the Post GEM Incubation Cleanup (Step 3.2), 45.5 μL of Elution Solution I is used to elute material from SPRIselect beads. 5 μL is used for GoT-ChA library construction, and the remaining 40 μL are used for ATAC library construction as indicated in the standard protocol. 3 - To generate the GoT-ChA library, two additional PCRs were performed on the 5 μL set aside during Step 3.2. The first PCR aims to amplify genotyping fragments prior to sample indexing and uses P5 (binds the P5 Illumina sequencing handle: AATGATACGGCGACCACCGAGATCTACAC) and GoT- ChA_nested (a nested, biotinylated, locus specific primer with a TruSeq Small RNA Read 2 handle: /5BiosG/CCTTGGCACCCGAGAATTCCA-[22bp locus specific]) primers with the following thermocycler program: 95 °C for 3 min; 15 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C. After a 1.2X SPRIselect clean up, biotinylated PCR product is bound and isolated using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher Scientific, #11206D). Briefly, beads are washed three times with 1X sodium chloride-sodium phosphate-EDTA buffer (SSPE, VWR, #VWRV0810- 4L), added to the purified PCR product, and incubated at room temperature for 15 minutes. The beads are then washed twice with 1X SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments are then amplified and sample indexed using P5 and RPI-X (binds the TruSeq Small RNA Read 2 handle and adds a sample index and P7 Illumina sequencing handle: CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGAC TGGAGTTCCTTGGCACCCGAGAATTCCA, “X” denotes user-defined sample index) primers with the following thermocycler program: 95 °C for 3 min; 6- 10 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C
GoT-ChA libraries were sequenced to 5,000 read pairs per nucleus

tag: sample description

value: Patient 6 - Processed with GoT-ChA-ASAP protocol

tag: mpn subtype

value: Myelofibrosis

value: Ruxolitinib


title: Replicate1_iWT

first: Dogukan

last: Mizrak

address: NCRC Building 26, 263S

department: Cardiac Surgery

data_processing:
BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.
The demultiplexed fastqs were analyzed using 10X Genomics Space Ranger using the following parameters --transcriptome=refdata-gex-GRCh38-2020-A --probe-set=Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv --r2-length=50
Assembly: GRCh38
Library strategy: spatial transcriptomic

extract_protocol:
FFPE Visium slides were deparaffinized and decrosslinked according to manufacturer's protocol (10X Genomics). Probe hybridization was performed using Visium Human Transcriptome probe kit. Probe ligation, release and extension were performed according to the manufacturer's protocol (10X Genomics)
The spatially barcoded ligated probe products were harvested and were indexed via Sample Index PCR per manufacturer's protocol (10X Genomics). The resulting libraries were cleaned up using SPRIselect and was subjected to 151bp paired-end sequencing on Illumina NovaSeq 6000.

tag: gender


title: Replicate1_Patient


title: Lac7_6_R1_P

description: miRNA

value: mammary gland

value: C57/BL6 female

value: lactation day 7


title: Time Point_0dpc_Group_PBS_Sample18

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: primary


title: P18_2_R1_P

description: miRNA


title: Time Point_0dpc_Group_PBS_Sample20

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Replicate2_Patient

data_processing:
BCL Convert Conversion Software v3.10.5 (Illumina) was used to generate de-multiplexed Fastq files.
The demultiplexed fastqs were analyzed using 10X Genomics Space Ranger using the following parameters --transcriptome=refdata-gex-GRCh38-2020-A --probe-set=Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv --r2-length=50
Assembly: GRCh38
Library strategy: spatial transcriptomic

extract_protocol:
FFPE Visium slides were deparaffinized and decrosslinked according to manufacturer's protocol (10X Genomics). Probe hybridization was performed using Visium Human Transcriptome probe kit. Probe ligation, release and extension were performed according to the manufacturer's protocol (10X Genomics)
The spatially barcoded ligated probe products were harvested and were indexed via Sample Index PCR per manufacturer's protocol (10X Genomics). The resulting libraries were cleaned up using SPRIselect and was subjected to 28x151bp paired-end sequencing on Illumina NovaSeq 6000.


title: Pt-07 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 7 - Myelofibrosis ruxolitinib-treated stage

value: Peripheral blood mononuclear cells (PBMC)

value: Fedratinib


title: P18_1_R1_P

description: miRNA

value: pregnancy day 18


title: Time Point_0dpc_Group_PBS_Sample16

value: 0 days post-challenge


title: Pt-02 (GoT-ChA-ASAP) [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 2 - Processed with GoT-ChA-ASAP protocol

value: Untreated


title: Serum sample of highly myopic patient IgG 14

description: IgG

value: Sera

tag: molecular

value: Autoantibody

value: Female


title: Serum sample of emmetropic control IgM 9

description: IgM

tag: age (years)


title: Pt-06 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 6 - Myelofibrosis ruxolitinib-treated stage

value: Myelofibrosis

value: Ruxolitinib


title: Serum sample of highly myopic patient IgG 9

description: IgG

tag: al


title: Serum sample of highly myopic patient IgG 8

description: IgG


title: Serum sample of highly myopic patient IgG 10

description: IgG

value: Male


title: Time Point_0dpc_Group_3dv_Sample15

value: 27 weeks old

value: ad libitum

value: Whole Blood

tag: time

value: Vaccination


title: Time Point_0dpc_Group_PBS_Sample17

tag: tissue

value: primary

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: 12E_S1

value: D1-expressing neuron

value: female


title: Lac7_4_R1_P

description: miRNA

value: mammary gland

value: C57/BL6 female

value: lactation day 7


title: Lac7_5_R1_P

description: miRNA


title: Time Point_0dpc_Group_3dv_Sample13

value: 0 days post-challenge

tag: treatment


title: Lac7_2_R1_P

description: miRNA

tag: cell type


title: Lac7_3_R1_P

description: miRNA


title: Time Point_0dpc_Group_3dv_Sample14


title: Pt-01 (MF-T1) [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

source_name: Bone marrow

value: Patient 1 - Myelofibrosis ruxolitinib-treated stage

value: Bone marrow


title: Serum sample of highly myopic patient IgG 5

description: IgG

value: Sera

value: Autoantibody


title: Serum sample of highly myopic patient IgG 7

description: IgG

value: Female


title: Pt-05 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 5 - Myelofibrosis ruxolitinib-treated stage

value: Myelofibrosis

value: Ruxolitinib


title: Serum sample of highly myopic patient IgG 11

description: IgG


title: Inv_5_R1_P

description: miRNA

value: involution day 3


title: Time Point_0dpc_Group_3dv_Sample12

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: primary

value: Vaccination


title: Serum sample of highly myopic patient IgG 4

description: IgG

value: Male


title: Pt-02 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 2 - Myelofibrosis untreated stage

value: Peripheral blood mononuclear cells (PBMC)

value: Untreated


title: KFO-20

value: primary pancreatic ductal adenocarcinoma (PDAC)


title: Pt-03 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 3 - Myelofibrosis untreated stage


title: Time Point_0dpc_Group_7dv_Sample10

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 0 days post-challenge


title: Pt-04 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 4 - Myelofibrosis untreated stage


title: Serum sample of highly myopic patient IgG 2

description: IgG

value: Sera

value: Autoantibody


title: Serum sample of highly myopic patient IgG 6

description: IgG

value: Female


title: Serum sample of highly myopic patient IgG 3

description: IgG


title: Inv_4_R1_P

description: miRNA

value: mammary gland

value: C57/BL6 female

value: involution day 3


title: Lac7_1_R1_P

description: miRNA

value: lactation day 7


title: Time Point_0dpc_Group_7dv_Sample9

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: primary

value: Vaccination


title: Inv_3_R1_P

description: miRNA


title: Serum sample of highly myopic patient IgG 12

description: IgG

value: Male


title: Time Point_0dpc_Group_3dv_Sample11


title: Inv_1_R1_P

description: miRNA


title: Pt-01 (MF-T0) [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 1 - Myelofibrosis untreated stage

value: Bone marrow

value: Myelofibrosis

value: Untreated


title: Serum sample of emmetropic control IgG 10

description: IgG

value: Sera


title: Serum sample of emmetropic control IgM 4

description: IgM

value: Autoantibody


title: Pt-01 (PV) [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

value: Patient 1 - Polycythemia Vera stage

value: Polycythemia Vera

value: Hydroxyurea


title: SM4 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

source_name: Cell line mixture 1:1:1 (HEL, SET-2 and CCRF-CEM)

value: Cell mixing experiment containing the HEL, SET-2 and CCRF-CEM cell lines targeting the JAK2V617 locus with GoT-ChA


title: Inv_2_R1_P

description: miRNA

value: mammary gland

value: C57/BL6 female

value: involution day 3


title: Inv_6_R1_P

description: miRNA


title: Time Point_0dpc_Group_7dv_Sample8

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: Peripheral Blood Mononuclear Cells (PBMCs)

value: 0 days post-challenge


title: Time Point_0dpc_Group_7dv_Sample7

value: primary

value: Vaccination


title: RM30 [Genotyping GoT-ChA amplicon]

description: Genotyping GoT-ChA amplicon

source_name: Cell line 1:1 mixture (HEL and CA46)

value: Cell mixing experiment containing the HEL and CA46 cell lines targeting the TP53R248 locus with GoT-ChA

value: Cell line 1:1 mixture (HEL and CA46)


title: AEL96, scRNA

city: Houston

first: Komal Kumar

last: Bollepogu Raja

state: TX

address: One Baylor plaza

department: Pathology and Immunology

institute: baylor college of medicine

description: 10X Genomics

data_processing:
scRNA-seq- The demultiplexing, barcode processing and initial QC was done using CellRanger aggr pipeline. Cell Ranger 6.01
Assembly: Dm6
Supplementary files format and content: scRNA-seq:Seurat object .rds file from R

organism: Drosophila melanogaster

source_name: eye disc

extract_protocol:
Eye discs from Drosophila larvae were dissected in 1X PBS on ice and dissociated using collagenase and dispase for ~40min. The dissociated cells were washed once with 1X PBS with 0.05% BSA. The cell pellet was resuspended in 1xPBS+0.05% BSA and viability was asayed using Hoechst-PI
Library was prepaed as per the manufacture's instructions. Single Cell 3' Reagent Kit v3.1 from 10x Genomics. Drosohila larval eye single cells were resuspended on master mix and GEMs were generated by loading the cells with partioning oil and gel beads with primers. The poly-A RNA was captured on the beads and reverse transcribed to generate cDNA which contains Illumina R1 primer sequence,10X barcode and a unique molecular identifier. The cDNA was purified and amplified by PCR. Illumina R2 primer sequence, paired-end constructs with P5 and P7 and sample index were added during library construction.

value: eye disc

tag: genotype

value: Wild type


title: AEL88, scRNA

description: 10X Genomics


title: AEL78, scRNA

description: 10X Genomics


title: Serum sample of emmetropic control IgG 9

description: IgG

value: Sera

value: Autoantibody

value: Female


title: Pt-02 (GoT-ChA-ASAP) [ATAC-seq]

description: Fragment file obtained after processing of raw sequencing files through the cell-ranger-atac (v2.0.0) pipeline

data_processing:
FASTQ files were processed through the cell-ranger-atac (v2.0.0). Single cell ATAC-seq metadata files were generated by analysis with ArchR (v1.0.0),  Gotcha (v1.0.0) and GotchaMito (v1.0.0)
Assembly: hg38
Supplementary files format and content: Fragment files output from cell-ranger-atac (v2.0.0) pipeline as tab separated files. Metadata including cell cluster and genotype assignments is available as .csv files.

growth_protocol: Cell lines were cultivated in the following conditions: HEL: ; SET-2: ; CCRF-CEM: ; CA46: .

extract_protocol:
Patient samples were FACS-sorted using CD34+ DAPI- gating. Downstream processing using the 10X Chromium Solution platform for single cell ATAC sequencing, with the modifications of the GoT-ChA protocol.
Nuclei were subsequently processed according to the Chromium Next GEM Single Cell ATAC Solution user guide (version CG000209 Rev F, 10x Genomics) with the following modifications: 1- During the GEM Generation and Barcoding reaction (Step 2.1), 1 μL of 22.5 μM GoT-ChA primer mix was added to the barcoding reaction mixture. The primers used are GoT-ChA_R1N (locus-specific primer with a Read 1N handle sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG - [22bp locus specific]) and GoT-ChA_IS2 (locus- specific primer with an IS2 handle sequence: AGCAAGTGAGAAGCATCGTGTC - [22bp locus specific]). These primers allow for exponential amplification of the GoT-ChA fragments, relative to the linear amplification of ATAC fragments. 2- During the Post GEM Incubation Cleanup (Step 3.2), 45.5 μL of Elution Solution I is used to elute material from SPRIselect beads. 5 μL is used for GoT-ChA library construction, and the remaining 40 μL are used for ATAC library construction as indicated in the standard protocol. 3 - To generate the GoT-ChA library, two additional PCRs were performed on the 5 μL set aside during Step 3.2. The first PCR aims to amplify genotyping fragments prior to sample indexing and uses P5 (binds the P5 Illumina sequencing handle: AATGATACGGCGACCACCGAGATCTACAC) and GoT- ChA_nested (a nested, biotinylated, locus specific primer with a TruSeq Small RNA Read 2 handle: /5BiosG/CCTTGGCACCCGAGAATTCCA-[22bp locus specific]) primers with the following thermocycler program: 95 °C for 3 min; 15 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C. After a 1.2X SPRIselect clean up, biotinylated PCR product is bound and isolated using Dynabeads M-280 Streptavidin magnetic beads (Thermo Fisher Scientific, #11206D). Briefly, beads are washed three times with 1X sodium chloride-sodium phosphate-EDTA buffer (SSPE, VWR, #VWRV0810- 4L), added to the purified PCR product, and incubated at room temperature for 15 minutes. The beads are then washed twice with 1X SSPE buffer and once with 10 mM Tris-HCl (pH 8.0) before resuspending in water. The bead-bound fragments are then amplified and sample indexed using P5 and RPI-X (binds the TruSeq Small RNA Read 2 handle and adds a sample index and P7 Illumina sequencing handle: CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGAC TGGAGTTCCTTGGCACCCGAGAATTCCA, “X” denotes user-defined sample index) primers with the following thermocycler program: 95 °C for 3 min; 6- 10 cycles of 95 °C for 20 s, 65°C for 30 s and 72°C for 20 s; followed by 72°C for 5 min and ending with hold at 4°C
ATAC libraries were sequenced to a depth of 25,000 read pairs per nucleus and GoT-ChA libraries were sequenced to 5,000 read pairs per nucleus

value: Patient 2 - Processed with GoT-ChA-ASAP protocol

value: Peripheral blood mononuclear cells (PBMC)

value: Myelofibrosis

value: Untreated


title: Time Point_0dpc_Group_12dv_Sample4

value: 27 weeks old

value: ad libitum

tag: cell line


title: Time Point_0dpc_Group_12dv_Sample5

value: Whole Blood

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Pt-06 (GoT-ChA-ASAP) [ATAC-seq]

value: Patient 6 - Processed with GoT-ChA-ASAP protocol

value: Ruxolitinib


title: Serum sample of emmetropic control IgG 8

description: IgG

value: Male


title: Serum sample of emmetropic control IgG 7

description: IgG


title: Pt-07 [ATAC-seq]

value: Patient 7 - Myelofibrosis ruxolitinib-treated stage

value: Fedratinib


title: Serum sample of highly myopic patient IgG 1

description: IgG


title: Serum sample of emmetropic control IgG 6

description: IgG


title: Pt-06 [ATAC-seq]

value: Patient 6 - Myelofibrosis ruxolitinib-treated stage


title: Serum sample of emmetropic control IgG 5

description: IgG

value: Sera


title: Time Point_0dpc_Group_7dv_Sample6

value: primary

value: 0 days post-challenge

value: Vaccination


title: AEL72, scRNA

description: 10X Genomics

value: eye disc

value: Wild type


title: Serum sample of emmetropic control IgG 4

description: IgG

value: Autoantibody


title: AEL69, scRNA

description: 10X Genomics


title: Pt-05 [ATAC-seq]

value: Patient 5 - Myelofibrosis ruxolitinib-treated stage

value: Bone marrow

value: Myelofibrosis


title: Time Point_0dpc_Group_12dv_Sample2

value: 27 weeks old

value: ad libitum

value: Whole Blood

value: Peripheral Blood Mononuclear Cells (PBMCs)


title: Time Point_0dpc_Group_12dv_Sample1


title: Replicate2_iWT

value: Female


title: Pt-01 (MF-T1) [ATAC-seq]

value: Patient 1 - Myelofibrosis ruxolitinib-treated stage

value: Ruxolitinib


title: Serum sample of emmetropic control IgG 3

description: IgG

value: Sera


title: S2 rep2

city: Singapore

first: KAIJING

last: CHEN

address: 60 Nanyang Drive

department: school of biological science

country: Singapore

institute: Nanyang Technological University

data_processing:
Adaptors were trimmed by TrimGalore (0.6.6) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Trimmed sequence reads were mapped to hg19 in pair-end mode using bowtie2 (v2.3.5.1) with default parameters.
The resulting SAM files were converted to BAM format and filtered to exclude reads with a mapq score below 30 using samtools (v1.10).
The BAM files were sorted, and duplicate reads were removed using through Picard (https://github.com/broadinstitute/picard, v 2.27.5-4).
After removing reads mapped to chrM, chrUn, and 'random' chromosomes, BAM files from replicates were merged.
Then merged bam files were converted to BigWig files with RPKM normalization using deeptools bamCoverage (v3.4.3) for data visualization on the UCSC Genome Browser.
Peaks were called using MACS2 (v2.2.7.1) (PMID: 24743991) callpeak with the following flag parameters: --shift -100 --extsize 200 --nomodel -B --SPMR -g hs, and peaks contained in the ENCODE (v2) hg19 blacklist were removed.
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak files were generated using MACS v2 with default settings.

growth_protocol: CRISPR knockout and K562 wild-type cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum, and 1% penicillin-streptomycin. All cultures were maintained at 37 °C, 5% CO2 in a humidified incubator.

extract_protocol:
ATAC-seq was performed using the Diagenode ATAC-seq Kit (C01080002, Diagenode) following the manufacturer’s protocol. Briefly, 200,000 EV, S1KO, S2KO and DKO K562 cells or 50,000 drug-treated cells per sample were harvested and nuclei were isolated. Immediately following the nuclei prep, the pellet was resuspended in 50 µl tagmentation mix. The transposition reaction was carried out for 30 min at 37C. The tagmented DNA was then purified and eluted in 12 µl of DNA Elution Buffer.
Library was constructed using 10 µl of tagmented DNA and 1 µl of primer pair provided by the 24 UDI for Tagmented libraries Set I (C01011034, Diagenode)  following the manufacturer’s protocol. Libraries were amplified using 11-16 cycles on the thermocycler. The DNA fragments with target sizes ranging from 200 bp to 1000 bp were selected using AMPure XP beads (Beckman Coulter) and validated using the Agilent High Sensitivity DNA kit.

treatment_protocol: EV, S1KO, S2KO and DKO K562 cells were generated using the all-in-one CRISPR/Cas9 vector system. K562 wild-type cells were either treated with 0.1% DMSO or combined treatment of GSK343 (5 uM) and X5050 (100 uM) for 72 hr.

value: knockout silencer2 region


title: Pt-04 [ATAC-seq]

value: Patient 4 - Myelofibrosis untreated stage

value: Peripheral blood mononuclear cells (PBMC)

value: Untreated


title: Pt-03 [ATAC-seq]

value: Patient 3 - Myelofibrosis untreated stage


title: AEL76, scRNA

description: 10X Genomics

value: eye disc

value: Wild type


title: S2 rep1


title: Serum sample of emmetropic control IgG 1

description: IgG

value: Autoantibody

value: Male